LCR-modules: a collection of workflows for cancer genome analysis.
other · Level V
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- Record sourced from PubMed, PMID 42271624.
- Also identified by DOI 10.1093/bioinformatics/btag366.
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Abstract
The surge of genomic data from advanced sequencing technologies is outpacing current analytical pipelines. We introduce LCR-modules, an open-source suite of bioinformatics tools designed for flexible and automated cancer genome data analysis. LCR-modules enables reproducible analysis of diverse cancer genomics data at scale. The suite comprises 49 Snakemake-based workflows organized into three levels, facilitating tasks from low-level quality control to complex cohort-level analyses. LCR-modules supports various sequencing types and integrates pipelines such as mutation calling, expression quantification, and cohort-level aggregation, ensuring flexibility and reproducibility. LCR-modules represents a significant advancement in genomic data analysis, reducing barriers in reproducibility and scalability and has already been applied to a combination of exomes and genomes from over 10,800 samples. No new data were generated in support of this research. The source code for the LCR-modules is openly available at https://github.com/LCR-BCCRC/lcr-modules. NA.